label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
label.do_not_display_again = Do not display this message again
exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
-exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
\ No newline at end of file
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+label.filter = Filter text:
+action.customfilter = Custom only
\ No newline at end of file
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
label.do_not_display_again = No mostrar este mensaje de nuevo
exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
-exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
\ No newline at end of file
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
+label.filter = Filter text:
+action.customfilter = Custom only
\ No newline at end of file
import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
import jalview.schemes.ColourSchemeProperty;
+import jalview.urls.UrlLinkTableModel;
import jalview.urls.UrlProvider;
import jalview.urls.UrlProviderI;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
+import javax.swing.RowSorter;
+import javax.swing.SortOrder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
*/
public static UrlProviderI sequenceUrlLinks;
+ public static UrlLinkTableModel dataModel;
+
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
* must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
UrlProviderI.DEFAULT_STRING);
sequenceUrlLinks = new UrlProvider(UrlProviderI.DEFAULT_LABEL, string);
+ List<String> colNames = new ArrayList<String>();
+ // colNames.add("ID");
+ // TODO KM add to properties file
+ colNames.add("URL");
+ colNames.add("In Menu");
+ colNames.add("Default");
+ dataModel = new UrlLinkTableModel(sequenceUrlLinks, colNames, "ID");
+
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
* .properties file as '|' separated strings
groupURLLinks = new ArrayList<String>();
}
- Vector<String> nameLinks, urlLinks;
-
JInternalFrame frame;
DasSourceBrowser dasSource;
/*
* Set Connections tab defaults
*/
- nameLinks = new Vector<String>();
- urlLinks = new Vector<String>();
- resetStoredLinks();
- updateLinkData();
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List<RowSorter.SortKey> sortKeys = new ArrayList<>();
+
+ sortKeys.add(new RowSorter.SortKey(3,
+ SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(2, SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(0, SortOrder.ASCENDING));
+
+ sorter.setSortKeys(sortKeys);
+ sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }
+
+ };
+ doReset.addActionListener(onReset);
+
+ // filter to display only custom urls
+ final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends TableModel, ? extends Object> entry)
+ {
+ String id = entry.getStringValue(4);
+ return sequenceUrlLinks.isUserEntry(id);
+ }
+ };
+
+ final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ customSorter.setRowFilter(customUrlFilter);
+
+ ActionListener onCustomOnly;
+ onCustomOnly = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(customUrlFilter);
+ }
+ };
+ userOnly.addActionListener(onCustomOnly);
+
+ filterTB.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+ });
+
+ // set up list selection functionality
+ linkUrlTable.getSelectionModel().addListSelectionListener(
+ new UrlListSelectionHandler());
+
+ // set up radio buttons
+ linkUrlTable.getColumn("Default").setCellRenderer(
+ new RadioButtonRenderer());
+ linkUrlTable.getColumn("Default")
+ .setCellEditor(new RadioButtonEditor());
+
+ // get boolean columns and resize those to min possible
+ for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
+ {
+ if (linkUrlTable.getModel().getColumnClass(column)
+ .equals(Boolean.class))
+ {
+ TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
+ column);
+ int preferredWidth = tableColumn.getMinWidth();
+
+ TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
+ column);
+ Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
+ int cwidth = c.getPreferredSize().width
+ + linkUrlTable.getIntercellSpacing().width;
+ preferredWidth = Math.max(preferredWidth, cwidth);
+
+ tableColumn.setPreferredWidth(preferredWidth);
+ }
+ }
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+ useProxy_actionPerformed(); // make sure useProxy is correctly initialised
proxyServerTB.setEnabled(useProxy.isSelected());
proxyPortTB.setEnabled(useProxy.isSelected());
proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
jalview.util.BrowserLauncher.resetBrowser();
// save user-defined and selected links
- String links = sequenceUrlLinks.writeUrlsAsString();
+ String links = linkUrlTable.getModel().toString();
if (links.isEmpty())
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
{
if (link.checkValid())
{
- nameLinks.addElement(link.getName());
- urlLinks.addElement(link.getURL());
- if (updateLinkData())
- {
- valid = true;
- }
- else
- {
- break;
- }
+ ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
+ link.getName(), link.getURL());
+ valid = true;
}
}
else
{
GSequenceLink link = new GSequenceLink();
- int index = linkNameList.getSelectedIndex();
+ int index = linkUrlTable.getSelectedRow();
if (index == -1)
{
+ // no row was selected
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
return;
}
- link.setName(nameLinks.elementAt(index).toString());
- link.setURL(urlLinks.elementAt(index).toString());
+ link.setName(linkUrlTable.getValueAt(index, 0).toString());
+ link.setURL(linkUrlTable.getValueAt(index, 1).toString());
boolean valid = false;
while (!valid)
{
if (link.checkValid())
{
- nameLinks.setElementAt(link.getName(), index);
- urlLinks.setElementAt(link.getURL(), index);
- if (updateLinkData())
- {
- valid = true;
- }
- else
- {
- break;
- }
+
+ linkUrlTable.setValueAt(link.getName(), index, 0);
+ linkUrlTable.setValueAt(link.getURL(), index, 1);
+ valid = true;
}
}
-
else
{
break;
@Override
public void deleteLink_actionPerformed(ActionEvent e)
{
- int index = linkNameList.getSelectedIndex();
+ int index = linkUrlTable.getSelectedRow();
+ int modelIndex = -1;
if (index == -1)
{
+ // no row is selected
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
- nameLinks.removeElementAt(index);
- urlLinks.removeElementAt(index);
- updateLinkData();
- }
-
- private boolean updateLinkData()
- {
- try
- {
- sequenceUrlLinks.setUrlLinks(nameLinks, urlLinks);
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
- } catch (IllegalArgumentException e)
+ else
{
-
- // put back the old links
- resetStoredLinks();
-
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- e.getMessage(), MessageManager.getString("label.link_name"),
- JOptionPane.WARNING_MESSAGE);
-
- return false;
+ modelIndex = linkUrlTable.convertRowIndexToModel(index);
}
- return true;
- }
- private void resetStoredLinks()
- {
- Vector<String> nlinks = sequenceUrlLinks.getLinksForDisplay();
-
- nameLinks.clear();
- urlLinks.clear();
- for (String entry : nlinks)
- {
- nameLinks.addElement(entry.split("\\|")[0]);
- urlLinks.addElement(entry.split("\\|")[1]);
- }
+ // make sure we use the model index to delete, and not the table index
+ ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
+
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
return name.hashCode() + code.hashCode();
}
}
+
+ private class UrlListSelectionHandler implements ListSelectionListener
+ {
+
+ @Override
+ public void valueChanged(ListSelectionEvent e)
+ {
+ ListSelectionModel lsm = (ListSelectionModel) e.getSource();
+
+ int index = lsm.getMinSelectionIndex();
+ if (index == -1)
+ {
+ // no selection, so disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+ return;
+ }
+ int modelIndex = linkUrlTable.convertRowIndexToModel(index);
+
+ // determine if the new selection is a custom url or not
+ if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable
+.getModel()
+ .getValueAt(modelIndex, 4))) // KM TODO do this better
+ {
+ // entry is not a user-defined url and so should not be edited
+ // disable edit and delete buttons
+ deleteLink.setEnabled(false);
+ editLink.setEnabled(false);
+ }
+ else
+ {
+ deleteLink.setEnabled(true);
+ editLink.setEnabled(true);
+ }
+
+ // BUT it's the default url, don't allow deletion
+ if ((boolean) linkUrlTable.getValueAt(index, 3))
+ {
+ deleteLink.setEnabled(false);
+ }
+ }
+}
}
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
-import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
+import javax.swing.JTable;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
import javax.swing.border.TitledBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
/**
* Base class for the Preferences panel.
/*
* Connections tab components
*/
- protected JList linkURLList = new JList();
+ protected JTable linkUrlTable = new JTable();
+
+ protected JButton editLink = new JButton();
+
+ protected JButton deleteLink = new JButton();
+
+ protected JTextField filterTB = new JTextField();
+
+ protected JButton doReset = new JButton();
+
+ protected JButton userOnly = new JButton();
+
+ protected JLabel portLabel = new JLabel();
+
+ protected JLabel serverLabel = new JLabel();
protected JTextField proxyServerTB = new JTextField();
protected JTextField defaultBrowser = new JTextField();
- protected JList linkNameList = new JList();
-
protected JCheckBox useProxy = new JCheckBox();
protected JCheckBox usagestats = new JCheckBox();
{
JPanel connectTab = new JPanel();
connectTab.setLayout(new GridBagLayout());
- JLabel serverLabel = new JLabel();
+
+ // Label for browser text box
+ JLabel browserLabel = new JLabel();
+ browserLabel.setFont(LABEL_FONT);
+ browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+ browserLabel.setText(MessageManager
+ .getString("label.default_browser_unix"));
+ defaultBrowser.setFont(LABEL_FONT);
+ defaultBrowser.setText("");
+
+ defaultBrowser.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ defaultBrowser_mouseClicked(e);
+ }
+ }
+ });
+
+ JPanel proxyPanel = initConnTabProxyPanel();
+ JPanel linkPanel = initConnTabUrlLinks();
+ initConnTabCheckboxes();
+
+ // Add URL link panel
+ connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 2.0, 2.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(
+ 16, 0, 0, 12), 359, 32));
+
+ // Add default Browser text box
+ connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(10, 0, 0, 0), 5, 1));
+
+ connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 0, 10), 307, 1));
+
+ // Add proxy server panel
+ connectTab.add(proxyPanel, new GridBagConstraints(0, 2, 2, 1, 1.0, 0.0,
+ GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 0, 12), 4, 10));
+
+ // Add usage stats, version check and questionnaire checkboxes
+ connectTab.add(usagestats, new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ connectTab.add(questionnaire, new GridBagConstraints(1, 3, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 10), 70, 1));
+ connectTab.add(versioncheck, new GridBagConstraints(0, 4, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ return connectTab;
+ }
+
+ /**
+ * Initialises the proxy server panel in the Connections tab
+ *
+ * @return the proxy server panel
+ */
+ private JPanel initConnTabProxyPanel()
+ {
+ // Label for server text box
serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
serverLabel.setFont(LABEL_FONT);
+
+ // Proxy server and port text boxes
proxyServerTB.setFont(LABEL_FONT);
proxyPortTB.setFont(LABEL_FONT);
- JLabel portLabel = new JLabel();
+
+ // Label for Port text box
portLabel.setFont(LABEL_FONT);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
portLabel.setText(MessageManager.getString("label.port"));
- JLabel browserLabel = new JLabel();
- browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager
- .getString("label.default_browser_unix"));
- defaultBrowser.setFont(LABEL_FONT);
- defaultBrowser.setText("");
+
+ // Use proxy server checkbox
+ useProxy.setFont(LABEL_FONT);
+ useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+ useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+ useProxy.setText(MessageManager.getString("label.use_proxy_server"));
+ useProxy.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useProxy_actionPerformed();
+ }
+ });
+
+ // Make proxy server panel
+ JPanel proxyPanel = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
+ proxyPanel.setBorder(titledBorder1);
+ proxyPanel.setLayout(new GridBagLayout());
+ proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 2, 0), 5, 0));
+ proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 0, 2, 0), 11, 0));
+ proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 5, 185), 2, -4));
+ proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 2), 54, 1));
+ proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 0), 263, 1));
+
+ return proxyPanel;
+ }
+
+ /**
+ * Initialises the checkboxes in the Connections tab
+ */
+ private void initConnTabCheckboxes()
+ {
+ // Usage stats checkbox label
usagestats.setText(MessageManager
.getString("label.send_usage_statistics"));
usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Questionnaire checkbox label
questionnaire.setText(MessageManager
.getString("label.check_for_questionnaires"));
questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Check for latest version checkbox label
versioncheck.setText(MessageManager
.getString("label.check_for_latest_version"));
versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ }
+
+ /**
+ * Initialises the URL links panel in the Connection tab
+ *
+ * @return the URL links panel
+ */
+ private JPanel initConnTabUrlLinks()
+ {
+ // Set up table for Url links
+ linkUrlTable.setFillsViewportHeight(true);
+ linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
+ linkUrlTable.setAutoCreateRowSorter(true);
+ linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ // Table in scrollpane so that the table is given a scrollbar
+ JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
+ linkScrollPane.setBorder(null);
+
+ // Panel for links functionality
+ JPanel linkPanel = new JPanel(new GridBagLayout());
+ linkPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.url_linkfrom_sequence_id")));
+
+ // Put the Url links panel together
+
+ // Buttons go at top right, resizing only resizes the blank space vertically
+ JPanel buttonPanel = initConnTabUrlButtons();
+ GridBagConstraints linkConstraints1 = new GridBagConstraints();
+ linkConstraints1.gridx = 1;
+ linkConstraints1.gridy = 0;
+ linkConstraints1.fill = GridBagConstraints.VERTICAL;
+ linkPanel.add(buttonPanel, linkConstraints1);
+
+ // Links table goes at top left, resizing resizes the table
+ GridBagConstraints linkConstraints2 = new GridBagConstraints();
+ linkConstraints2.gridx = 0;
+ linkConstraints2.gridy = 0;
+ linkConstraints2.weightx = 1.0;
+ linkConstraints2.weighty = 1.0;
+ linkConstraints2.fill = GridBagConstraints.BOTH;
+ linkPanel.add(linkScrollPane, linkConstraints2);
+
+ // Filter box and buttons goes at bottom left, resizing resizes the text box
+ JPanel filterPanel = initConnTabFilterPanel();
+ GridBagConstraints linkConstraints3 = new GridBagConstraints();
+ linkConstraints3.gridx = 0;
+ linkConstraints3.gridy = 1;
+ linkConstraints3.weightx = 1.0;
+ linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
+ linkPanel.add(filterPanel, linkConstraints3);
+
+ return linkPanel;
+ }
+
+ private JPanel initConnTabFilterPanel()
+ {
+ // Filter textbox and reset button
+ JLabel filterLabel = new JLabel(
+ MessageManager.getString("label.filter"));
+ filterLabel.setFont(LABEL_FONT);
+ filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ filterTB.setFont(LABEL_FONT);
+ filterTB.setText("");
+
+ doReset.setText(MessageManager.getString("action.reset"));
+ userOnly.setText(MessageManager.getString("action.customfilter"));
+
+ // Panel for filter functionality
+ JPanel filterPanel = new JPanel(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+
+ filterPanel.add(filterLabel, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 0;
+ gbc1.gridx = 1;
+ gbc1.fill = GridBagConstraints.HORIZONTAL;
+ gbc1.anchor = GridBagConstraints.WEST;
+ gbc1.weightx = 1.0;
+ filterPanel.add(filterTB, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 2;
+ gbc2.fill = GridBagConstraints.NONE;
+ gbc2.anchor = GridBagConstraints.WEST;
+ filterPanel.add(doReset, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 3;
+ gbc3.fill = GridBagConstraints.NONE;
+ gbc3.anchor = GridBagConstraints.WEST;
+ filterPanel.add(userOnly, gbc3);
+
+ return filterPanel;
+ }
+
+ private JPanel initConnTabUrlButtons()
+ {
+ // Buttons for new / edit / delete Url links
JButton newLink = new JButton();
newLink.setText(MessageManager.getString("action.new"));
newLink.addActionListener(new java.awt.event.ActionListener()
newLink_actionPerformed(e);
}
});
- JButton editLink = new JButton();
+
editLink.setText(MessageManager.getString("action.edit"));
editLink.addActionListener(new java.awt.event.ActionListener()
{
editLink_actionPerformed(e);
}
});
- JButton deleteLink = new JButton();
+
deleteLink.setText(MessageManager.getString("action.delete"));
deleteLink.addActionListener(new java.awt.event.ActionListener()
{
}
});
- linkURLList.addListSelectionListener(new ListSelectionListener()
- {
- @Override
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkURLList.getSelectedIndex();
- linkNameList.setSelectedIndex(index);
- }
- });
+ // no current selection, so initially disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
- linkNameList.addListSelectionListener(new ListSelectionListener()
- {
- @Override
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkNameList.getSelectedIndex();
- linkURLList.setSelectedIndex(index);
- }
- });
+ // Panels for new/edit/delete link buttons
+ // buttonContent prevents the buttons from being resized when the window is
+ JPanel buttonContent = new JPanel(new GridLayout(0, 1, 0, 0));
+ JPanel buttonPanel = new JPanel(new BorderLayout());
- JScrollPane linkScrollPane = new JScrollPane();
- linkScrollPane.setBorder(null);
- JPanel linkPanel = new JPanel();
- linkPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.url_linkfrom_sequence_id")));
- linkPanel.setLayout(new BorderLayout());
- GridLayout gridLayout1 = new GridLayout();
- JPanel editLinkButtons = new JPanel();
- editLinkButtons.setLayout(gridLayout1);
- gridLayout1.setRows(3);
- linkNameList.setFont(LABEL_FONT);
- linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- BorderLayout borderLayout3 = new BorderLayout();
- JPanel linkPanel2 = new JPanel();
- linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(LABEL_FONT);
- linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ buttonContent.add(newLink, null);
+ buttonContent.add(editLink, null);
+ buttonContent.add(deleteLink, null);
+ buttonPanel.add(buttonContent, BorderLayout.NORTH);
- defaultBrowser.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- defaultBrowser_mouseClicked(e);
- }
- }
- });
- useProxy.setFont(LABEL_FONT);
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText(MessageManager.getString("label.use_proxy_server"));
- useProxy.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- useProxy_actionPerformed();
- }
- });
- linkPanel.add(editLinkButtons, BorderLayout.EAST);
- editLinkButtons.add(newLink, null);
- editLinkButtons.add(editLink, null);
- editLinkButtons.add(deleteLink, null);
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);
- linkScrollPane.getViewport().add(linkPanel2, null);
- linkPanel2.add(linkURLList, BorderLayout.CENTER);
- linkPanel2.add(linkNameList, BorderLayout.WEST);
- JPanel jPanel1 = new JPanel();
- TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.proxy_server"));
- jPanel1.setBorder(titledBorder1);
- jPanel1.setLayout(new GridBagLayout());
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 4, 0), 5, 0));
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 4, 0), 11, 6));
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 16, 0, 0, 12), 359, -17));
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 21, 0, 35, 12), 4, 6));
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(16, 0, 0, 0), 5, 1));
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 54, 1));
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 0), 263, 1));
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(15, 0, 0, 15), 307, 1));
- connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- return connectTab;
+ return buttonPanel;
}
/**
public void useProxy_actionPerformed()
{
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
+ boolean enabled = useProxy.isSelected();
+ portLabel.setEnabled(enabled);
+ serverLabel.setEnabled(enabled);
+ proxyServerTB.setEnabled(enabled);
+ proxyPortTB.setEnabled(enabled);
}
+ public class RadioButtonRenderer extends JRadioButton implements
+ TableCellRenderer
+ {
+ public RadioButtonRenderer()
+ {
+ setHorizontalAlignment(CENTER);
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ setSelected((boolean) value);
+
+ // set colours to match rest of table
+ if (isSelected)
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+
+ // adjust row height so radio buttons actually fit
+ table.setRowHeight(row, getMinimumSize().height);
+
+ return this;
+ }
+ }
+
+ public class RadioButtonEditor extends AbstractCellEditor implements
+ TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
+
+ public RadioButtonEditor()
+ {
+ this.button.setHorizontalAlignment(SwingConstants.CENTER);
+ this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fireEditingStopped();
+ }
+ });
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable table,
+ Object value, boolean isSelected, int row, int column)
+ {
+ button.setSelected((boolean) value);
+ return button;
+ }
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return button.isSelected();
+ }
+
+ }
}
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
-import java.awt.Panel;
import java.awt.Rectangle;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
-public class GSequenceLink extends Panel
+public class GSequenceLink extends JPanel
{
public GSequenceLink()
{
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.StringTokenizer;
import java.util.Vector;
while (st.hasMoreElements())
{
String name = st.nextToken();
- String url = st.nextToken();
- // check for '|' within a regex
- int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
- if (rxstart == -1)
- {
- rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
- }
- while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
- && st.hasMoreTokens())
+
+ if (!isMiriamId(name))
{
- url = url + SEP + st.nextToken();
+ // this one of our custom urls
+ String url = st.nextToken();
+ // check for '|' within a regex
+ int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
+ if (rxstart == -1)
+ {
+ rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
+ }
+ while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
+ && st.hasMoreTokens())
+ {
+ url = url + SEP + st.nextToken();
+ }
+ urls.put(name, new UrlLink(name + SEP + url));
}
- urls.put(name, new UrlLink(name + SEP + url));
}
} catch (Exception ex)
{
}
@Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+ for (Entry<String, UrlLink> entry : urls.entrySet())
+ {
+ String key = entry.getKey();
+ boolean isDefault = (key.equals(defaultUrl));
+ boolean isSelected = true; // custom urls always selected
+ String displayLink = entry.getValue().toString().split("\\|")[1]; // TODO
+ // sort
+ // this
+ // out
+ // properly!
+ displayLinks.add(new UrlLinkDisplay(key, key, displayLink,
+ isSelected,
+ isDefault));
+ }
+ return displayLinks;
+ }
+
+ @Override
public boolean setDefaultUrl(String id)
{
if (urls.containsKey(id))
}
@Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ HashMap<String, UrlLink> newurls = new HashMap<String, UrlLink>();
+
+ Iterator<UrlLinkDisplay> it = links.iterator();
+ while (it.hasNext())
+ {
+ UrlLinkDisplay link = it.next();
+
+ // MIRIAM ids will be handled by a different UrlProvider class
+ if (!isMiriamId(link.getId()))
+ {
+
+ // don't allow duplicate key names as entries will be overwritten
+ if (newurls.containsKey(link.getId()))
+ {
+ throw new IllegalArgumentException(MessageManager.formatMessage(
+ "exception.url_cannot_have_duplicate_id", link.getId()));
+ }
+ if (link.getIsSelected())
+ {
+ newurls.put(link.getId(),
+ new UrlLink(link.getId() + SEP + link.getUrl()));
+
+ // sort out default and selected ids
+ if (link.getIsDefault())
+ {
+ setDefaultUrl(link.getId());
+ }
+ }
+ // TODO KM make it possible to set and save selected custom urls
+
+ }
+
+ }
+ urls = newurls;
+ }
+
+ @Override
public String chooseDefaultUrl()
{
// unilaterally set the default id to the EMBL_EBI link
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
import java.util.Vector;
import org.json.simple.JSONArray;
{
// File idFile = getIdentifiers();
urls = readIdentifiers(new FileReader(idFileName));
+ selectedUrls = new ArrayList<String>();
checkSelectionMatchesUrls(cachedUrlList);
} catch (IOException e)
{
-
+ System.out.println("Exception reading URLs from identifiers.org");
+ System.out.println(e.getMessage());
}
}
private void checkSelectionMatchesUrls(String cachedUrlList)
{
- selectedUrls = new ArrayList<String>();
+
String[] prevSelected = cachedUrlList.split("\\" + SEP);
for (String id : prevSelected)
{
private void checkSelectionMatchesUrls(Vector<String> idList)
{
- selectedUrls = new ArrayList<String>();
String[] prevSelected = new String[idList.size()];
idList.toArray(prevSelected);
for (String id : prevSelected)
@Override
public String writeUrlsAsString()
{
- StringBuffer links = new StringBuffer();
- for (String k : selectedUrls)
+ if (!selectedUrls.isEmpty())
{
- links.append(k);
+ StringBuffer links = new StringBuffer();
+ for (String k : selectedUrls)
+ {
+ links.append(k);
+ links.append(SEP);
+ }
+ // remove last SEP
+ links.setLength(links.length() - 1);
+ return links.toString();
}
- return links.toString();
+ return "";
}
@Override
Vector<String> links = new Vector<String>();
for (String key : selectedUrls)
{
- links.add(key + SEP + urls.get(key).get("url") + "/" + DELIM
+ links.add(urls.get(key).get("name") + SEP + urls.get(key).get("url")
+ + "/" + DELIM
+ DB_ACCESSION + DELIM);
}
return links;
}
@Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+ for (Entry<String, HashMap<String, String>> entry : urls.entrySet())
+ {
+ String key = entry.getKey();
+ boolean isDefault = (key == defaultUrl);
+ boolean isSelected = (selectedUrls.contains(key));
+ displayLinks.add(new UrlLinkDisplay(key,
+ entry.getValue().get("name"),
+ entry.getValue().get("url")
+ + "/" + DELIM + DB_ACCESSION + DELIM, isSelected, isDefault));
+ }
+ return displayLinks;
+ }
+
+ @Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ selectedUrls = new ArrayList<String>();
+
+ Iterator<UrlLinkDisplay> it = links.iterator();
+ while (it.hasNext())
+ {
+ UrlLinkDisplay link = it.next();
+
+ // Handle links with MIRIAM ids only
+ if (isMiriamId(link.getId())) // TODO separate use of name and id
+ {
+ // select/deselect links accordingly and set default url
+
+ if (link.getIsSelected())
+ {
+ if (urls.containsKey(link.getId()))
+ {
+ selectedUrls.add(link.getId());
+ }
+ if (link.getIsDefault())
+ {
+ setDefaultUrl(link.getId());
+ }
+
+ }
+ }
+
+ }
+ }
+
+ @Override
public String getDefaultUrl(String seqid)
{
return urls.get(defaultUrl).get("url") + "/" + seqid;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+
+/**
+ * UrlLink table row definition
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+
+public class UrlLinkDisplay
+{
+ private String id; // id is not supplied to display, but used to identify
+ // entries when saved
+
+ private String name;
+
+ private String url;
+
+ private boolean isDefault;
+
+ private boolean isSelected;
+
+ public final static int ID = 4;
+
+ public final static int URL = 1;
+
+ public final static int SELECTED = 2;
+
+ public final static int DEFAULT = 3;
+
+ public final static int NAME = 0;
+
+ public UrlLinkDisplay(String rowId, String rowName, String rowUrl,
+ boolean rowSelected, boolean rowDefault)
+ {
+ id = rowId;
+ name = rowName;
+ url = rowUrl;
+ isDefault = rowDefault;
+ isSelected = rowSelected;
+ }
+
+ public String getId()
+ {
+ return id;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public String getUrl()
+ {
+ return url;
+ }
+
+ public boolean getIsDefault()
+ {
+ return isDefault;
+ }
+
+ public boolean getIsSelected()
+ {
+ return isSelected;
+ }
+
+ public void setUrl(String rowUrl)
+ {
+ url = rowUrl;
+ }
+
+ public void setIsDefault(boolean rowDefault)
+ {
+ isDefault = rowDefault;
+ }
+
+ public void setIsSelected(boolean rowSelected)
+ {
+ isSelected = rowSelected;
+ }
+
+ public Object getValue(int index)
+ {
+ switch (index)
+ {
+ case ID:
+ return id;
+ case URL:
+ return url;
+ case DEFAULT:
+ return isDefault;
+ case SELECTED:
+ return isSelected;
+ case NAME:
+ return name;
+ default:
+ return null; // TODO
+ }
+ }
+
+ public void setValue(int index, Object value)
+ {
+ switch (index)
+ {
+ case ID:
+ id = (String) value;
+ break;
+ case URL:
+ url = (String) value;
+ break;
+ case DEFAULT:
+ isDefault = (boolean) value;
+ break;
+ case SELECTED:
+ isSelected = (boolean) value;
+ break;
+ case NAME:
+ name = (String) value;
+ break;
+ default:
+ // TODO
+ }
+ }
+
+ public boolean isEditable(int index)
+ {
+ return ((index == DEFAULT) || (index == SELECTED));
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.table.AbstractTableModel;
+
+/**
+ * TableModel for UrlLinks table
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+
+public class UrlLinkTableModel extends AbstractTableModel
+{
+ // local storage of data
+ // use LinkedHashMap to guarantee ordering remains the same, as
+ // we need to maintain a row/col mapping into the HashMap
+ private List<UrlLinkDisplay> data;
+
+ private UrlProviderI dataProvider;
+
+ private List<String> displayColumns;
+
+ // row in table which is currently the default
+ private int defaultRow;
+
+ /**
+ * UrlLinkTableModel constructor
+ *
+ * @param baseData
+ * base data set to be presented in table
+ * @param entryNames
+ * keys of entries in baseData's nested hashmap. Should match order
+ * in displayColNames
+ * @param displayColNames
+ * names of columns to display in order.
+ * @param keyColName
+ * name of column corresponding to keys in baseData
+ */
+ public UrlLinkTableModel(UrlProviderI baseData,
+ List<String> displayColNames,
+ String keyColName)
+ {
+ dataProvider = baseData;
+ data = baseData.getLinksForTable();
+ displayColumns = new ArrayList<String>();
+ displayColumns.add(keyColName);
+ displayColumns.addAll(displayColNames);
+
+ // find the default row
+ defaultRow = 0;
+ Iterator<UrlLinkDisplay> it = data.iterator();
+ while (it.hasNext())
+ {
+ if (it.next().getIsDefault())
+ {
+ break;
+ }
+ else
+ {
+ defaultRow++;
+ }
+ }
+ }
+
+ @Override
+ public int getRowCount()
+ {
+ if (data == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return data.size();
+ }
+ }
+
+ @Override
+ public int getColumnCount()
+ {
+ return displayColumns.size();
+ }
+
+ @Override
+ public Object getValueAt(int rowIndex, int columnIndex)
+ {
+ return data.get(rowIndex).getValue(columnIndex);
+ }
+
+ @Override
+ public boolean isCellEditable(int rowIndex, int columnIndex)
+ {
+ return data.get(rowIndex).isEditable(columnIndex);
+ }
+
+ @Override
+ public void setValueAt(Object aValue, int rowIndex, int columnIndex)
+ {
+ if ((columnIndex == UrlLinkDisplay.SELECTED)
+ && (rowIndex == defaultRow))
+ {
+ // Selected urls column: can't deselect default URL
+ // refuse to edit: TODO show message box here
+
+ }
+ else if (columnIndex == UrlLinkDisplay.DEFAULT)
+ {
+ // Default url column: exactly one row must always be true
+ if (rowIndex != defaultRow)
+ {
+ // selected row is not currently the default
+ // set the current default to false
+ data.get(defaultRow).setValue(columnIndex, false);
+ fireTableRowsUpdated(defaultRow, defaultRow);
+
+ // set the default to be the selected row
+ defaultRow = rowIndex;
+ data.get(rowIndex).setValue(columnIndex, aValue);
+
+ // default row must also be selected
+ if (!data.get(rowIndex).getIsSelected())
+ {
+ data.get(rowIndex).setValue(UrlLinkDisplay.SELECTED, true);
+ }
+ fireTableRowsUpdated(rowIndex, rowIndex);
+ }
+ }
+ else
+ {
+ data.get(rowIndex).setValue(columnIndex, aValue);
+ fireTableRowsUpdated(rowIndex, rowIndex);
+ }
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ return getValueAt(0, columnIndex).getClass();
+ }
+
+ @Override
+ public String getColumnName(int columnIndex)
+ {
+ return displayColumns.get(columnIndex);
+ }
+
+ @Override
+ public String toString()
+ {
+ // update the UrlProvider from data list
+ dataProvider.setUrlData(data);
+
+ return dataProvider.writeUrlsAsString();
+ }
+
+ public void removeRow(int rowIndex)
+ {
+ // remove the row from data
+ data.remove(rowIndex);
+
+ // update default row
+ if (defaultRow > rowIndex)
+ {
+ defaultRow--;
+ }
+
+ fireTableRowsDeleted(rowIndex, rowIndex);
+ }
+
+ public int insertRow(String name, String url)
+ {
+ // add a row to the data
+ UrlLinkDisplay u = new UrlLinkDisplay(name, name, url, true, false);
+ int index = data.size();
+ data.add(u);
+ fireTableRowsInserted(index, index);
+ return index;
+ }
+}
*/
package jalview.urls;
+import static jalview.util.UrlConstants.SEP;
+
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
UrlProviderI idProvider = new IdentifiersUrlProvider(cachedUrlList,
ID_ORG_FILE);
customProvider = new CustomUrlProvider(cachedUrlList);
- // providers.add(idProvider);
+ providers.add(idProvider);
providers.add(customProvider);
// check that the defaultUrl still exists
for (UrlProviderI p : providers)
{
result += p.writeUrlsAsString();
+ result += SEP;
}
+ // remove last sep
+ result = result.substring(0, result.length() - 1);
return result;
}
}
@Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+ for (UrlProviderI p : providers)
+ {
+ displayLinks.addAll(p.getLinksForTable());
+ }
+ return displayLinks;
+ }
+
+ @Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ for (UrlProviderI p : providers)
+ {
+ p.setUrlData(links);
+ }
+ }
+
+ @Override
public String getDefaultUrl(String seqid)
{
String link = null;
return customProvider.chooseDefaultUrl();
}
+ @Override
+ public boolean isUserEntry(String id)
+ {
+ return customProvider.isUserEntry(id);
+ }
}
package jalview.urls;
import java.io.File;
+import java.util.List;
import java.util.Vector;
/**
Vector<String> getLinksForDisplay();
/**
+ * Get names and urls as strings for display
+ *
+ */
+ List<UrlLinkDisplay> getLinksForTable();
+
+ /**
+ * Set names and urls from display settings
+ */
+ void setUrlData(List<UrlLinkDisplay> links);
+
+ /**
* Get the id of the default URL
*
* @return id of the default URL
* @return id of chosen default url
*/
String chooseDefaultUrl();
+
+ /**
+ * Determine if id is for a user-defined URL
+ */
+ boolean isUserEntry(String id);
}
*/
package jalview.urls;
+import java.util.List;
import java.util.Vector;
import java.util.regex.Pattern;
+/**
+ * Leaf node of UrlProvider composite
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+
public class UrlProviderImpl implements UrlProviderI
{
private static final Pattern MIRIAM_PATTERN = Pattern
return null;
}
+ @Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ return null;
+ }
+
+ @Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ // deliberately left empty
+ }
+
protected boolean isMiriamId(String id)
{
return MIRIAM_PATTERN.matcher(id).matches();
}
-
+ @Override
+ public boolean isUserEntry(String id)
+ {
+ return !isMiriamId(id);
+ }
}
git://source.jalview.org / jalview.git / commitdiff